Minfi preprocessing and rs probes
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@gustavo-fernandez-bayon-5300
Last seen 5.4 years ago
Spain
Hi everybody. I have just noticed that some probes disappeared during my workflow with minfi. When I looked into the preprocessing, I saw that preprocessIllumina() ends up calling preprocessRaw() in order to generate M and U signals. The interesting part is, only probes of type I and II are used for that. I noticed that the probes that were disappearing in my workflow are of type 'SNPI' and 'SNPII'. Now I know in which part the probes are lost, but I would like to know the reason behind this procedure. Also, could anybody give me a hint if this is what Genomestudio is doing? What are this rs* probes useful for then? Regards, Gus --------------------------- Enviado con Sparrow (http://www.sparrowmailapp.com/?sig)
Preprocessing minfi Preprocessing minfi • 1.4k views
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@kasper-daniel-hansen-2979
Last seen 6 months ago
United States
The 'rs' probes are normal SNP probes; they do not measure methylation. Quoting from the Illumina methylation guide "rs# representsSNPassays (not affected by DNA methylation)" and "SNP assays can be used for sample identification and tracking. They should be excluded for differential methylation analysis." The purpose of these probes is for catching sample mix-ups. We have decided to remove them from the methylation object (MethylSet) because they do not measure methylation and the purpose of this object is to contain the methylation measurements. Kasper On Wed, Nov 21, 2012 at 4:38 AM, Gustavo Fern?ndez Bay?n <gbayon at="" gmail.com=""> wrote: > Hi everybody. > > I have just noticed that some probes disappeared during my workflow with minfi. When I looked into the preprocessing, I saw that preprocessIllumina() ends up calling preprocessRaw() in order to generate M and U signals. The interesting part is, only probes of type I and II are used for that. I noticed that the probes that were disappearing in my workflow are of type 'SNPI' and 'SNPII'. > > Now I know in which part the probes are lost, but I would like to know the reason behind this procedure. Also, could anybody give me a hint if this is what Genomestudio is doing? What are this rs* probes useful for then? > > Regards, > Gus > > > > --------------------------- > Enviado con Sparrow (http://www.sparrowmailapp.com/?sig) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Hi Kasper. It's perfectly clear for me now what rs* probes are. I should have read the Illumina guide before, I guess. But it is always a pleasure to ask in this list and learn a little bit more. I agree with your decision about removing the probes. Problem is, GenomeStudio is calculating the betas for those probes too, which is something I think can lead to confusion. In my humble opinion, if something is not measuring methylation, showing a beta value for it on your interface is going to make a new user go mad (as has effectively happened to a fellow biologist in my lab). I have another question. I was wondering about opening a new topic, but I think it might fit in this context. Why is minfi not using the correction constant 100 in the denominator when calculating the betas? I have always wondered about that constant, because I did not see the exact reasoning behind it, and I am inclined to think more in your way o implementing it. In the end, it really makes no difference, doesn't it? Regards, Gus --------------------------- Enviado con Sparrow (http://www.sparrowmailapp.com/?sig) El mi?rcoles 21 de noviembre de 2012 a las 17:35, Kasper Daniel Hansen escribi?: > The 'rs' probes are normal SNP probes; they do not measure > methylation. Quoting from the Illumina methylation guide > "rs# representsSNPassays (not affected by DNA methylation)" > and > "SNP assays can be used for sample identification and tracking. They > > should be excluded for differential methylation analysis." > > The purpose of these probes is for catching sample mix-ups. We have > decided to remove them from the methylation object (MethylSet) because > they do not measure methylation and the purpose of this object is to > contain the methylation measurements. > > Kasper > > > > > On Wed, Nov 21, 2012 at 4:38 AM, Gustavo Fern?ndez Bay?n > <gbayon at="" gmail.com="" (mailto:gbayon="" at="" gmail.com)=""> wrote: > > Hi everybody. > > > > I have just noticed that some probes disappeared during my workflow with minfi. When I looked into the preprocessing, I saw that preprocessIllumina() ends up calling preprocessRaw() in order to generate M and U signals. The interesting part is, only probes of type I and II are used for that. I noticed that the probes that were disappearing in my workflow are of type 'SNPI' and 'SNPII'. > > > > Now I know in which part the probes are lost, but I would like to know the reason behind this procedure. Also, could anybody give me a hint if this is what Genomestudio is doing? What are this rs* probes useful for then? > > > > Regards, > > Gus > > > > > > > > --------------------------- > > Enviado con Sparrow (http://www.sparrowmailapp.com/?sig) > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org (mailto:Bioconductor at r-project.org) > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
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On Thu, Nov 22, 2012 at 2:50 AM, Gustavo Fern?ndez Bay?n <gbayon at="" gmail.com=""> wrote: > > Hi Kasper. > > It's perfectly clear for me now what rs* probes are. I should have read the Illumina guide before, I guess. But it is always a pleasure to ask in this list and learn a little bit more. > > I agree with your decision about removing the probes. Problem is, GenomeStudio is calculating the betas for those probes too, which is something I think can lead to confusion. In my humble opinion, if something is not measuring methylation, showing a beta value for it on your interface is going to make a new user go mad (as has effectively happened to a fellow biologist in my lab). Glad that we agree. If you (or anyone else) have an awesome application for the rs probes, feel free to tell us. > I have another question. I was wondering about opening a new topic, but I think it might fit in this context. Why is minfi not using the correction constant 100 in the denominator when calculating the betas? I have always wondered about that constant, because I did not see the exact reasoning behind it, and I am inclined to think more in your way o implementing it. In the end, it really makes no difference, doesn't it? Well, they are trying to avoid a divide by zero problem. Whether or not that is important to handle also depends on how the data was normalized. It is easy to imagine a normalization procedure that makes sure that this never happens (for example a procedure that bounds all probe intensities away from zero). For such a normalization procedure, adding 100 makes little sense. In our implementation, you can choose to add a 100, but that default is zero. For most probes this should make no difference, but there may be a few where it matters. Kasper > Regards, > Gus > > --------------------------- > Enviado con Sparrow (http://www.sparrowmailapp.com/?sig) > > > El mi?rcoles 21 de noviembre de 2012 a las 17:35, Kasper Daniel Hansen escribi?: > >> The 'rs' probes are normal SNP probes; they do not measure >> methylation. Quoting from the Illumina methylation guide >> "rs# representsSNPassays (not affected by DNA methylation)" >> and >> "SNP assays can be used for sample identification and tracking. They >> >> should be excluded for differential methylation analysis." > >> >> The purpose of these probes is for catching sample mix-ups. We have >> decided to remove them from the methylation object (MethylSet) because >> they do not measure methylation and the purpose of this object is to >> contain the methylation measurements. >> >> Kasper >> >> >> >> >> On Wed, Nov 21, 2012 at 4:38 AM, Gustavo Fern?ndez Bay?n >> <gbayon at="" gmail.com="" (mailto:gbayon="" at="" gmail.com)=""> wrote: >> > Hi everybody. >> > >> > I have just noticed that some probes disappeared during my workflow with minfi. When I looked into the preprocessing, I saw that preprocessIllumina() ends up calling preprocessRaw() in order to generate M and U signals. The interesting part is, only probes of type I and II are used for that. I noticed that the probes that were disappearing in my workflow are of type 'SNPI' and 'SNPII'. >> > >> > Now I know in which part the probes are lost, but I would like to know the reason behind this procedure. Also, could anybody give me a hint if this is what Genomestudio is doing? What are this rs* probes useful for then? >> > >> > Regards, >> > Gus >> > >> > >> > >> > --------------------------- >> > Enviado con Sparrow (http://www.sparrowmailapp.com/?sig) >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org (mailto:Bioconductor at r-project.org) >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > >
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